A review on quantitative multiplexed proteomics

N Pappireddi, L Martin, M Wühr - Chembiochem, 2019 - Wiley Online Library
Over the last few decades, mass spectrometry‐based proteomics has become an
increasingly powerful tool that is now able to routinely detect and quantify thousands of …

Bioinformatics methods for mass spectrometry-based proteomics data analysis

C Chen, J Hou, JJ Tanner, J Cheng - International journal of molecular …, 2020 - mdpi.com
Recent advances in mass spectrometry (MS)-based proteomics have enabled tremendous
progress in the understanding of cellular mechanisms, disease progression, and the …

dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts

V Demichev, L Szyrwiel, F Yu, GC Teo… - Nature …, 2022 - nature.com
The dia-PASEF technology uses ion mobility separation to reduce signal interferences and
increase sensitivity in proteomic experiments. Here we present a two-dimensional peak …

Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform

F Yu, GC Teo, AT Kong, K Fröhlich, GX Li… - Nature …, 2023 - nature.com
Liquid chromatography (LC) coupled with data-independent acquisition (DIA) mass
spectrometry (MS) has been increasingly used in quantitative proteomics studies. Here, we …

Global detection of human variants and isoforms by deep proteome sequencing

P Sinitcyn, AL Richards, RJ Weatheritt… - Nature …, 2023 - nature.com
An average shotgun proteomics experiment detects approximately 10,000 human proteins
from a single sample. However, individual proteins are typically identified by peptide …

Mammalian retrovirus-like protein PEG10 packages its own mRNA and can be pseudotyped for mRNA delivery

M Segel, B Lash, J Song, A Ladha, CC Liu, X Jin… - Science, 2021 - science.org
Eukaryotic genomes contain domesticated genes from integrating viruses and mobile
genetic elements. Among these are homologs of the capsid protein (known as Gag) of long …

[HTML][HTML] Proteogenomic characterization of pancreatic ductal adenocarcinoma

L Cao, C Huang, DC Zhou, Y Hu, TM Lih, SR Savage… - Cell, 2021 - cell.com
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor patient
survival. Toward understanding the underlying molecular alterations that drive PDAC …

Transcription factors interact with RNA to regulate genes

O Oksuz, JE Henninger, R Warneford-Thomson… - Molecular cell, 2023 - cell.com
Transcription factors (TFs) orchestrate the gene expression programs that define each cell's
identity. The canonical TF accomplishes this with two domains, one that binds specific DNA …

A proximity-dependent biotinylation map of a human cell

CD Go, JDR Knight, A Rajasekharan, B Rathod… - Nature, 2021 - nature.com
Compartmentalization is a defining characteristic of eukaryotic cells, and partitions distinct
biochemical processes into discrete subcellular locations. Microscopy and biochemical …

Phase separation drives aberrant chromatin looping and cancer development

JH Ahn, ES Davis, TA Daugird, S Zhao, IY Quiroga… - Nature, 2021 - nature.com
The development of cancer is intimately associated with genetic abnormalities that target
proteins with intrinsically disordered regions (IDRs). In human haematological malignancies …